19.Sep.2009

19.Jul.2009

27.Nov.2008

contents

links

Introduction

The Pathway Projector was implemented according to the aforementioned requirements,
including the availability of a large-scale comprehensive pathway map, pathways from
a wide variety of organisms, and searching and mapping capabilities.
Since it has been implemented as a web application, this software is cross-platform
and requires no installation or maintenance. Moreover, use of the AJAX web development
paradigm provides an intuitive user experience similar to that of desktop applications.
The main pathway map of Pathway Projector was reconstructed from the popular KEGG Atlas
layout by adding nodes for enzymes and genes. As an example, the map for E. coli K12
contains 1365 genes, 1813 enzymes, and 1572 metabolites. Circular and rectangular nodes
represent metabolites and genes/enzymes, respectively, and the
names of genes, enzymes, and metabolites are displayed within the map at high zoom
levels by means of semantic zooming. Reaction edges are color coded according to the
following pathway categories: aqua represents glycan biosynthesis and metabolism, blue
represents carbohydrate metabolism, green represents lipid metabolism, red represents
nucleotide metabolism, purple represents energy metabolism, yellow represents amino
acid metabolism, pink represents metabolism of cofactors and vitamins, dark red represents
biosynthesis of secondary metabolites, orange represents metabolism of other amino
acids, and magenta represents biodegradation and metabolism of xenobiotics. Pathway
Projector utilizes the Google Maps API for the implementation of zoomable user interface (ZUI) and enables
smooth navigation through panning and zooming without page transitions using a mouse
scroll wheel or double clicks. Every component in the pathway map shows more detailed
information by clicking on the nodes, which opens up an information window containing
annotations, such as chemical and structural formulas and links to external public
databases. Users can therefore use Pathway Projector as a generic browser
and as a gateway for various pathway-related resources.

Software

start Pathway Projector

Documentations

Publication

Our manuscript describing this online resource is published by PLoS one journal with the title,
"Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API".
Click the above
Publication
to view the full-text of the manuscript.

License

Important Notice:
The software automatically utilizes KEGG data on the server side.
Academic users may freely download the KEGG data as
provided at the GenomeNet ftp site at ftp://ftp.genome.ad.jp/pub/kegg/, but non-academic users are requested to obtain a license agreement through the licensor, Pathway Solutions Inc., for installation of KEGG at their sites, for distribution or reselling of KEGG data, for software development and any other commercial activities that make use of KEGG, and also as end users of the third-party programs that access the KEGG ftp site.